apps/workbench/app/controllers/collections_controller.rb

   1 class CollectionsController < ApplicationController
   2   skip_around_filter(:require_thread_api_token,
   3                      only: [:show_file, :show_file_links])
   4   skip_before_filter(:find_object_by_uuid,
   5                      only: [:provenance, :show_file, :show_file_links])
   6   # We depend on show_file to display the user agreement:
   7   skip_before_filter :check_user_agreements, only: :show_file
   8   skip_before_filter :check_user_profile, only: :show_file
   9
  10   RELATION_LIMIT = 5
  11
  12   def show_pane_list
  13     %w(Files Provenance_graph Used_by Advanced)
  14   end
  15
  16   def set_persistent
  17     case params[:value]
  18     when 'persistent', 'cache'
  19       persist_links = Link.filter([['owner_uuid', '=', current_user.uuid],
  20                                    ['link_class', '=', 'resources'],
  21                                    ['name', '=', 'wants'],
  22                                    ['tail_uuid', '=', current_user.uuid],
  23                                    ['head_uuid', '=', @object.uuid]])
  24       logger.debug persist_links.inspect
  25     else
  26       return unprocessable "Invalid value #{value.inspect}"
  27     end
  28     if params[:value] == 'persistent'
  29       if not persist_links.any?
  30         Link.create(link_class: 'resources',
  31                     name: 'wants',
  32                     tail_uuid: current_user.uuid,
  33                     head_uuid: @object.uuid)
  34       end
  35     else
  36       persist_links.each do |link|
  37         link.destroy || raise
  38       end
  39     end
  40
  41     respond_to do |f|
  42       f.json { render json: @object }
  43     end
  44   end
  45
  46   def choose
  47     # Find collections using default find_objects logic, then search for name
  48     # links, and preload any other links connected to the collections that are
  49     # found.
  50     # Name links will be obsolete when issue #3036 is merged,
  51     # at which point this entire custom #choose function can probably be
  52     # eliminated.
  53
  54     params[:limit] ||= 40
  55
  56     find_objects_for_index
  57     @collections = @objects
  58
  59     @filters += [['link_class','=','name'],
  60                  ['head_uuid','is_a','arvados#collection']]
  61
  62     @objects = Link
  63     find_objects_for_index
  64
  65     @name_links = @objects
  66
  67     @objects = Collection.
  68       filter([['uuid','in',@name_links.collect(&:head_uuid)]])
  69
  70     preload_links_for_objects (@collections.to_a + @objects.to_a)
  71     super
  72   end
  73
  74   def index
  75     # API server index doesn't return manifest_text by default, but our
  76     # callers want it unless otherwise specified.
  77     @select ||= Collection.columns.map(&:name)
  78     base_search = Collection.select(@select)
  79     if params[:search].andand.length.andand > 0
  80       tags = Link.where(any: ['contains', params[:search]])
  81       @collections = (base_search.where(uuid: tags.collect(&:head_uuid)) |
  82                       base_search.where(any: ['contains', params[:search]])).
  83         uniq { |c| c.uuid }
  84     else
  85       if params[:limit]
  86         limit = params[:limit].to_i
  87       else
  88         limit = 100
  89       end
  90
  91       if params[:offset]
  92         offset = params[:offset].to_i
  93       else
  94         offset = 0
  95       end
  96
  97       @collections = base_search.limit(limit).offset(offset)
  98     end
  99     @links = Link.limit(1000).
 100       where(head_uuid: @collections.collect(&:uuid))
 101     @collection_info = {}
 102     @collections.each do |c|
 103       @collection_info[c.uuid] = {
 104         tag_links: [],
 105         wanted: false,
 106         wanted_by_me: false,
 107         provenance: [],
 108         links: []
 109       }
 110     end
 111     @links.each do |link|
 112       @collection_info[link.head_uuid] ||= {}
 113       info = @collection_info[link.head_uuid]
 114       case link.link_class
 115       when 'tag'
 116         info[:tag_links] << link
 117       when 'resources'
 118         info[:wanted] = true
 119         info[:wanted_by_me] ||= link.tail_uuid == current_user.uuid
 120       when 'provenance'
 121         info[:provenance] << link.name
 122       end
 123       info[:links] << link
 124     end
 125     @request_url = request.url
 126
 127     render_index
 128   end
 129
 130   def show_file_links
 131     Thread.current[:reader_tokens] = [params[:reader_token]]
 132     return if false.equal?(find_object_by_uuid)
 133     render layout: false
 134   end
 135
 136   def show_file
 137     # We pipe from arv-get to send the file to the user.  Before we start it,
 138     # we ask the API server if the file actually exists.  This serves two
 139     # purposes: it lets us return a useful status code for common errors, and
 140     # helps us figure out which token to provide to arv-get.
 141     coll = nil
 142     tokens = [Thread.current[:arvados_api_token], params[:reader_token]].compact
 143     usable_token = find_usable_token(tokens) do
 144       coll = Collection.find(params[:uuid])
 145     end
 146     if usable_token.nil?
 147       return  # Response already rendered.
 148     elsif params[:file].nil? or not file_in_collection?(coll, params[:file])
 149       return render_not_found
 150     end
 151     opts = params.merge(arvados_api_token: usable_token)
 152     ext = File.extname(params[:file])
 153     self.response.headers['Content-Type'] =
 154       Rack::Mime::MIME_TYPES[ext] || 'application/octet-stream'
 155     self.response.headers['Content-Length'] = params[:size] if params[:size]
 156     self.response.headers['Content-Disposition'] = params[:disposition] if params[:disposition]
 157     self.response_body = file_enumerator opts
 158   end
 159
 160   def sharing_scopes
 161     ["GET /arvados/v1/collections/#{@object.uuid}", "GET /arvados/v1/collections/#{@object.uuid}/", "GET /arvados/v1/keep_services/accessible"]
 162   end
 163
 164   def search_scopes
 165     begin
 166       ApiClientAuthorization.filter([['scopes', '=', sharing_scopes]]).results
 167     rescue ArvadosApiClient::AccessForbiddenException
 168       nil
 169     end
 170   end
 171
 172   def show
 173     return super if !@object
 174     if current_user
 175       jobs_with = lambda do |conds|
 176         Job.limit(RELATION_LIMIT).where(conds)
 177           .results.sort_by { |j| j.finished_at || j.created_at }
 178       end
 179       @output_of = jobs_with.call(output: @object.portable_data_hash)
 180       @log_of = jobs_with.call(log: @object.portable_data_hash)
 181       @project_links = Link.limit(RELATION_LIMIT).order("modified_at DESC")
 182         .where(head_uuid: @object.uuid, link_class: 'name').results
 183       project_hash = Group.where(uuid: @project_links.map(&:tail_uuid)).to_hash
 184       @projects = project_hash.values
 185
 186       if @object.uuid.match /[0-9a-f]{32}/
 187         @same_pdh = Collection.filter([["portable_data_hash", "=", @object.portable_data_hash]])
 188         owners = @same_pdh.map {|s| s.owner_uuid}.to_a
 189         preload_objects_for_dataclass Group, owners
 190         preload_objects_for_dataclass User, owners
 191       end
 192
 193       @permissions = Link.limit(RELATION_LIMIT).order("modified_at DESC")
 194         .where(head_uuid: @object.uuid, link_class: 'permission',
 195                name: 'can_read').results
 196       @logs = Log.limit(RELATION_LIMIT).order("created_at DESC")
 197         .where(object_uuid: @object.uuid).results
 198       @is_persistent = Link.limit(1)
 199         .where(head_uuid: @object.uuid, tail_uuid: current_user.uuid,
 200                link_class: 'resources', name: 'wants')
 201         .results.any?
 202       @search_sharing = search_scopes
 203     end
 204
 205     if params["tab_pane"] == "Provenance_graph"
 206       @prov_svg = ProvenanceHelper::create_provenance_graph(@object.provenance, "provenance_svg",
 207                                                             {:request => request,
 208                                                               :direction => :bottom_up,
 209                                                               :combine_jobs => :script_only}) rescue nil
 210     end
 211     if params["tab_pane"] == "Used_by"
 212       @used_by_svg = ProvenanceHelper::create_provenance_graph(@object.used_by, "used_by_svg",
 213                                                                {:request => request,
 214                                                                  :direction => :top_down,
 215                                                                  :combine_jobs => :script_only,
 216                                                                  :pdata_only => true}) rescue nil
 217     end
 218     super
 219   end
 220
 221   def sharing_popup
 222     @search_sharing = search_scopes
 223     respond_to do |format|
 224       format.html
 225       format.js
 226     end
 227   end
 228
 229   helper_method :download_link
 230
 231   def download_link
 232     collections_url + "/download/#{@object.uuid}/#{@search_sharing.first.api_token}/"
 233   end
 234
 235   def share
 236     a = ApiClientAuthorization.create(scopes: sharing_scopes)
 237     @search_sharing = search_scopes
 238     render 'sharing_popup'
 239   end
 240
 241   def unshare
 242     @search_sharing = search_scopes
 243     @search_sharing.each do |s|
 244       s.destroy
 245     end
 246     @search_sharing = search_scopes
 247     render 'sharing_popup'
 248   end
 249
 250   protected
 251
 252   def find_usable_token(token_list)
 253     # Iterate over every given token to make it the current token and
 254     # yield the given block.
 255     # If the block succeeds, return the token it used.
 256     # Otherwise, render an error response based on the most specific
 257     # error we encounter, and return nil.
 258     most_specific_error = [401]
 259     token_list.each do |api_token|
 260       begin
 261         using_specific_api_token(api_token) do
 262           yield
 263           return api_token
 264         end
 265       rescue ArvadosApiClient::ApiError => error
 266         if error.api_status >= most_specific_error.first
 267           most_specific_error = [error.api_status, error]
 268         end
 269       end
 270     end
 271     case most_specific_error.shift
 272     when 401, 403
 273       redirect_to_login
 274     when 404
 275       render_not_found(*most_specific_error)
 276     end
 277     return nil
 278   end
 279
 280   def file_in_collection?(collection, filename)
 281     target = CollectionsHelper.file_path(File.split(filename))
 282     collection.manifest.each_file.any? do |file_spec|
 283       CollectionsHelper.file_path(file_spec) == target
 284     end
 285   end
 286
 287   def file_enumerator(opts)
 288     FileStreamer.new opts
 289   end
 290
 291   class FileStreamer
 292     include ArvadosApiClientHelper
 293     def initialize(opts={})
 294       @opts = opts
 295     end
 296     def each
 297       return unless @opts[:uuid] && @opts[:file]
 298
 299       env = Hash[ENV].dup
 300
 301       require 'uri'
 302       u = URI.parse(arvados_api_client.arvados_v1_base)
 303       env['ARVADOS_API_HOST'] = "#{u.host}:#{u.port}"
 304       env['ARVADOS_API_TOKEN'] = @opts[:arvados_api_token]
 305       env['ARVADOS_API_HOST_INSECURE'] = "true" if Rails.configuration.arvados_insecure_https
 306
 307       IO.popen([env, 'arv-get', "#{@opts[:uuid]}/#{@opts[:file]}"],
 308                'rb') do |io|
 309         while buf = io.read(2**16)
 310           yield buf
 311         end
 312       end
 313       Rails.logger.warn("#{@opts[:uuid]}/#{@opts[:file]}: #{$?}") if $? != 0
 314     end
 315   end
 316 end